curvesplus package

Submodules

curvesplus.biobb_curves module

Module containing the Curves class and the command line interface.

class curvesplus.biobb_curves.Curves(input_struc_path, output_lis_path, output_cda_path, output_zip_path=None, input_top_path=None, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_dna Curves
Wrapper for the Cur+ executable that is part of the Curves+ software suite.
The Cur+ program is used to analyze the structure of nucleic acids and their complexes.
Parameters:

  • input_struc_path (str) – Trajectory or PDB input file. File type: input. Sample file. Accepted formats: trj (edam:format_3910), pdb (edam:format_1476), netcdf (edam:format_3650), nc (edam:format_3650).

  • input_top_path (str) (Optional) –

    Topology file, needed along with .trj file (optional). File type: input. Sample file. Accepted formats: top (edam:format_3881), pdb (edam:format_1476).

  • output_cda_path (str) –

    Filename for Curves+ output .cda file. File type: output. Sample file. Accepted formats: cda (edam:format_2330).

  • output_lis_path (str) –

    Filename for Curves+ output .lis file. File type: output. Sample file. Accepted formats: lis (edam:format_2330).

  • output_zip_path (str) (Optional) –

    Filename for .zip files containing Curves+ output that is not .cda or .lis files. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

  • properties (dict) –

    • s1range (str) - (None) Range of first strand. Must be specified in the form “start:end”.

    • s2range (str) - (None) Range of second strand. Must be specified in the form “start:end”.

    • stdlib_path (str) - (‘standard’) Path to Curves’ standard library files for nucleotides. If not specified will look for ‘standard’ files in current directory.

    • itst (int) - (0) Iteration start index.

    • itnd (int) - (0) Iteration end index.

    • itdel (int) - (1) Iteration delimiter.

    • ions (bool) - (False) If True, helicoidal analysis of ions (or solvent molecules) around solute is carried out.

    • test (bool) - (False) If True, provide addition output in .lis file on fitting and axis generation.

    • line (bool) - (False) if True, find the best linear helical axis.

    • fit (bool) - (True) if True, fit a standard bases to the input coordinates (important for MD snapshots to avoid base distortions leading to noisy helical parameters).

    • axfrm (bool) - (False) if True, generates closely spaced helical axis frames as input for Canal and Canion.

    • binary_path (str) - (Cur+) Path to Curves+ executable, otherwise the program wil look for Cur+ executable in the binaries folder.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

Examples

This is a use example of how to use the building block from Python:

from biobb_dna.curvesplus.biobb_curves import biobb_curves
prop = {
    's1range': '1:12',
    's2range': '24:13',
}
biobb_curves(
    input_struc_path='/path/to/structure/file.trj',
    input_top_path='/path/to/topology/file.top',
    output_cda_path='/path/to/output/file.cda',
    output_lis_path='/path/to/output/file.lis',
    properties=prop)
Info:
create_curvesplus_folder()[source]

Create .curvesplus folder in the current temporal folder and copy the lib files inside.

launch() → int[source]

Execute the Curves object.

curvesplus.biobb_curves.biobb_curves(input_struc_path: str, output_lis_path: str, output_cda_path: str, input_top_path: str | None = None, output_zip_path: str | None = None, properties: dict | None = None, **kwargs) → int[source]

Create Curves class and execute the launch() method.

curvesplus.biobb_curves.main()[source]

Command line execution of this building block. Please check the command line documentation.

curvesplus.biobb_canal module

Module containing the Canal class and the command line interface.

class curvesplus.biobb_canal.Canal(input_cda_file, input_lis_file=None, output_zip_path=None, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_dna Canal
Wrapper for the Canal executable that is part of the Curves+ software suite.
The Canal program is used to analyze the curvature of DNA structures.
Parameters:

  • input_cda_file (str) –

    Input cda file, from Cur+ output. File type: input. Sample file. Accepted formats: cda (edam:format_2330).

  • input_lis_file (str) (Optional) – Input lis file, from Cur+ output. File type: input. Accepted formats: lis (edam:format_2330).

  • output_zip_path (str) –

    zip filename for output files. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

  • properties (dic) –

    • bases (str) - (None) sequence of bases to be searched for in the I/P data (default is blank, meaning no specified sequence).

    • itst (int) - (0) Iteration start index.

    • itnd (int) - (0) Iteration end index.

    • itdel (int) - (1) Iteration delimiter.

    • lev1 (int) - (0) Lower base level limit (i.e. base pairs) used for analysis.

    • lev2 (int) - (0) Upper base level limit used for analysis. If lev1 > 0 and lev2 = 0, lev2 is set to lev1 (i.e. analyze lev1 only). If lev1=lev2=0, lev1 is set to 1 and lev2 is set to the length of the oligmer (i.e. analyze all levels).

    • nastr (str) - (‘NA’) character string used to indicate missing data in .ser files.

    • cormin (float) - (0.6) minimal absolute value for printing linear correlation coefficients between pairs of analyzed variables.

    • series (bool) - (False) if True then output spatial or time series data. Only possible for the analysis of single structures or single trajectories.

    • histo (bool) - (False) if True then output histogram data.

    • corr (bool) - (False) if True than output linear correlation coefficients between all variables.

    • sequence (str) - (Optional) sequence of the first strand of the corresponding DNA fragment, for each .cda file. If not given it will be parsed from .lis file.

    • binary_path (str) - (‘Canal’) Path to Canal executable, otherwise the program wil look for Canal executable in the binaries folder.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

Examples

This is a use example of how to use the building block from Python:

from biobb_dna.curvesplus.biobb_canal import biobb_canal
prop = {
    'series': 'True',
    'histo': 'True',
    'sequence': 'CGCGAATTCGCG'
}
biobb_canal(
    input_cda_file='/path/to/curves/output.cda',
    output_zip_path='/path/to/output.zip',
    properties=prop)
Info:
launch() → int[source]

Execute the Canal object.

curvesplus.biobb_canal.biobb_canal(input_cda_file: str, output_zip_path: str, input_lis_file: str | None = None, properties: dict | None = None, **kwargs) → int[source]

Create Canal class and execute the launch() method.

curvesplus.biobb_canal.main()[source]

Command line execution of this building block. Please check the command line documentation.

curvesplus.canal_unzip module

Module containing the CanalUnzip class and the command line interface.

class curvesplus.canal_unzip.CanalUnzip(input_zip_file, output_path, output_list_path=None, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_dna CanalUnzip
Tool for extracting biobb_canal output files.
Unzips a Canal output file contained within a zip file.
Parameters:

  • input_zip_file (str) –

    Zip file with Canal output files. File type: input. Sample file. Accepted formats: zip (edam:format_3987).

  • output_path (str) –

    Canal output file contained within input_zip_file. File type: output. Sample file. Accepted formats: ser (edam:format_2330), his (edam:format_3905), cor (edam:format_3465).

  • output_list_path (str) (Optional) –

    Text file with a list of all Canal output files contained within input_zip_file. File type: output. Sample file. Accepted formats: txt (edam:format_2330).

  • properties (dic) –

    • type (str) - (None) Type of file. Values: series, histo, corr.

    • helpar_name (str) - (None) Helical parameter name, only for ‘series’ and ‘histo’ types. Values: alphaC, alphaW, ampC, ampW, ax-bend, betaC, betaW, buckle, chiC, chiW, curv, deltaC, deltaW, epsilC, epsilW, gammaC, gammaW, h-ris, h-twi, inclin, majd, majw, mind, minw, opening, phaseC, phaseW, propel, reg, rise, roll, shear, shift, slide, stagger, stretch, tbend, tilt, tip, twist, xdisp, ydisp, zetaC, zetaW.

    • correlation (str) - (None) Correlation indexes separated by underscore (ie ‘98_165’), only for ‘corr’ type.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

Examples

This is a use example of how to use the building block from Python:

from biobb_dna.curvesplus.canal_unzip import canal_unzip
prop = {
    'type': 'series',
    'helpar_name': 'alphaC'
}
canal_unzip(
    input_zip_file='/path/to/canal/output.zip',
    output_path='/path/to/output.ser',
    output_list_path='/path/to/output.txt'
    properties=prop)
Info:
launch() → int[source]

Execute the CanalUnzip object.

curvesplus.canal_unzip.canal_unzip(input_zip_file: str, output_path: str, output_list_path: str | None = None, properties: dict | None = None, **kwargs) → int[source]

Create CanalUnzip class and execute the launch() method.

curvesplus.canal_unzip.main()[source]

Command line execution of this building block. Please check the command line documentation.

curvesplus.biobb_canion module

Module containing the Canion class and the command line interface.

class curvesplus.biobb_canion.Canion(input_cdi_path, input_afr_path, input_avg_struc_path, output_zip_path=None, properties=None, **kwargs)[source]

Bases: BiobbObject

biobb_dna Canion
Wrapper for the Canion executable that is part of the Curves+ software suite.
Analyzes the trajectory of ions around a DNA molecule.
Parameters:

  • input_cdi_path (str) –

    Trajectory input file. File type: input. Sample file. Accepted formats: cdi (edam:format_2330).

  • input_afr_path (str) –

    Helical axis frames corresponding to the input conformation to be analyzed. File type: input. Sample file. Accepted formats: afr (edam:format_2330).

  • input_avg_struc_path (str) –

    Average DNA conformation. File type: input. Sample file. Accepted formats: pdb (edam:format_1476).

  • output_zip_path (str) –

    Filename for .zip files containing Canion output files. File type: output. Sample file. Accepted formats: zip (edam:format_3987).

  • properties (dict) –

    • bases (str) - (None) Sequence of bases to be analyzed (default is blank, meaning no specified sequence).

    • type (str) - (‘*’) Ions (or atoms) to be analyzed. Options are ‘Na+’, ‘K’, ‘K+’, ‘Cl’, ‘Cl-’, ‘CL’, ‘P’, ‘C1*’, ‘NH1’, ‘NH2’, ‘NZ’, ‘1’ for all cations, ‘-1’ for all anions, ‘0’ for neutral species or ‘*’ for all available data.

    • dlow (float) - (0) Select starting segment of the oglimer to analyze. If both dhig and dlow are 0, entire oglimer is analyzed.

    • dhig (float) - (0) Select ending segment of the oglimer to analyze, being the maximum value the total number of base pairs in the oligomer. If both dhig and dlow are 0, entire oglimer is analyzed.

    • rlow (float) - (0) Minimal distances from the helical axis taken into account in the analysis.

    • rhig (float) - (0) Maximal distances from the helical axis taken into account in the analysis.

    • alow (float) - (0) Minimal angle range to analyze.

    • ahig (float) - (360) Maximal angle range to analyze.

    • itst (int) - (0) Number of first snapshot to be analyzed.

    • itnd (int) - (0) Number of last snapshot to be analyzed.

    • itdel (int) - (1) Spacing between analyzed snapshots.

    • rmsf (bool) - (False) If set to True uses the combination of the helical ion parameters and an average helical axis to map the ions into Cartesian space and then calculates their average position (pdb output) and their root mean square fluctuation values (rmsf output). A single pass rmsf algorithm to make this calculation possible with a single read of the trajectory file. This option is generally used for solute atoms and not for solvent molecules or ions.

    • circ (bool) - (False) If set to True, minicircles are analyzed.

    • binary_path (str) - (Canion) Path to Canion executable, otherwise the program wil look for Canion executable in the binaries folder.

    • remove_tmp (bool) - (True) [WF property] Remove temporal files.

    • restart (bool) - (False) [WF property] Do not execute if output files exist.

    • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

Examples

This is a use example of how to use the building block from Python:

from biobb_dna.curvesplus.biobb_canion import biobb_canion
prop = {
    'type': 'K+',
    'bases': 'G'
}
biobb_canion(
    input_cdi_path='/path/to/input.cdi',
    input_afr_path='/path/to/input.afr',
    input_avg_struc_path='/path/to/input.pdb',
    output_zip_path='/path/to/output.zip',
    properties=prop)
Info:
launch() → int[source]

Execute the Canion object.

curvesplus.biobb_canion.biobb_canion(input_cdi_path: str, input_afr_path: str, input_avg_struc_path: str, output_zip_path: str | None = None, properties: dict | None = None, **kwargs) → int[source]

Create Canion class and execute the launch() method.

curvesplus.biobb_canion.main()[source]

Command line execution of this building block. Please check the command line documentation.